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cld is not able to access the gene_list.txt file (and will presumably also fail to read the params.txt).
Command used to run cld:
`docker run -v $PWD boutroslab/cld_docker cld --task=end_to_end -…
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Hello,
I'm trying to use this implementation to do some analysis on pooled KO-CRISPR experiment with 10 samples divided in two groups: control and treatment. For each sample I have the amount of gu…
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Hi,
I'm trying to install the local version of CRISPOR, but getting the following error. Can you help me?
python crispor.py sacCer3 sampleFiles/in/sample.sacCer3.fa sampleFiles/mine/sample.sacCer3…
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Hi there! I have a library that contains a very large amplicon with two different insertion sites, and I had two questions regarding using crispresso on this.
1. Is it possible to visualize the entir…
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Hi
I have a query related to how tools are run in the nanocompore pipeline. Since your protocol is latest, I still wish to confirm if I need to make some changes according to what has been describ…
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https://mp.weixin.qq.com/s/QXZgq-kefkiX1GwtKxvIUw
ixxmu updated
2 months ago
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Heyhey!
I've been playing around with Milo for the analysis of a pooled single-cell CRISPR screen in the format of CROP/pertrub-seq. From what I understand through the tutorials, Milo requires tha…
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Hi,
For `sci-Plex`, the cell barcode position is not a fixed value.
R1: { **9-10 bp** hairpin barcode }-{CAGAGC}-{ 8bp UMI }--{10 bp RT barcode}
How could I generate the `readTable` for this read…
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I wrote my own program to count the occurrences of sgRNA sequences in fastq files before I found 2FAST2Q. When trying your program, however, the counts I get are different from my own program. After i…
th-of updated
6 months ago
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I have already removed the spurious pools of barcodes that weren't in the experiment.
Do we need/want all the extant columns? They are:
design | dialout | gene_id | gene_symbol | oligo | sgRNA | sou…